Question: Could not find or load main class net.sf.picard.sam.SortSam
0
gravatar for blur
22 months ago by
blur90
European Union
blur90 wrote:

Hi,

I am trying to run a protocol from a paper in nature, and I am stuck with this step: The commands parameters are as described in the paper, but I get an error msg "Error: Could not find or load main class net.sf.picard.sam.SortSam"

anyone have any idea what I am doing wrong?

java -Xmx2048m -XX:+UseParallelOldGC -XX:ParallelGCThreads=4 -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -Djava.io.tmpdir=/nadata/users/me/ -cp /nadata/software/GATK_3.6/GenomeAnalysisTK.jar net.sf.picard.sam.SortSam INPUT=/nadata/users/me/B_RBFOX2_R1.fastq.adaptorTrim_round2_rmRep_reDup.bam TMP_DIR=/nadata/users/me/ OUTPUT=/nadata/users/mor/ECLIP/RBFOX2/B_RBFOX2_R1.fastq.adaptorTrim_round2_rmRep_reDup_sorted.bam VALIDATION_STRINGENCY=SILENT SO=coordinate CREATE_INDEX=true
    Error: Could not find or load main class net.sf.picard.sam.SortSam

Thanks!

rna-seq chip-seq • 812 views
ADD COMMENTlink modified 19 months ago by 3468716630 • written 22 months ago by blur90

It would be helpful if you also post the link to the paper and in which section it is described. (BTW, it is just a typo here right? ava insetad of java)

ADD REPLYlink written 22 months ago by venu6.1k

yeah, that was a typo... it is taken from this paper: Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP) http://www.nature.com/nmeth/journal/v13/n6/full/nmeth.3810.html from Nature

ADD REPLYlink modified 22 months ago • written 22 months ago by blur90

I also do the same thing of that, did you use samtools sort instead ?

ADD REPLYlink written 19 months ago by 3468716630

Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your post but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

ADD REPLYlink written 19 months ago by WouterDeCoster37k

I'm new to here, really think you !

ADD REPLYlink written 19 months ago by 3468716630
0
gravatar for Pierre Lindenbaum
22 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum118k wrote:

there is no such net.sf.picard.sam.SortSam in GATK (tested with 3.7)

   $  jar tvf GenomeAnalysisTK.jar | grep SortSam

SortSam is not part of the package net.sf.picard.sam since a long time: https://github.com/broadinstitute/picard/blob/master/src/main/java/picard/sam/SortSam.java (but picard.sam )

what you want is not GATK but picard : https://github.com/broadinstitute/picard/releases/tag/2.9.2

java -jar picard.jar SortSam

furthermore, samtools sort is faster

ADD COMMENTlink modified 22 months ago • written 22 months ago by Pierre Lindenbaum118k

I tried substituting the link to GATK with a link to Picard but it didn't work... I also did samtools sort, and it worked like charm, but I'd still like to know why this didn't work...

ADD REPLYlink written 22 months ago by blur90
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